Genome browser (IGV)

Genome browser

Genome browsers allow us to look at the read support for sequencing-based assays. In transcriptomics, this would be looking at the reads that are evidence of the expression of a gene; showing both read alignments and known annotations for a gene's location on the genome. We show an example of the read-support for GAD2 in Brain MD70. To view it live, please click on this link, log in, and go to downloads where you can click on the BAM to view it.

This visualization shows several tracks (rows) of data showing the read-support of GAD2 expression in the selected BAM. At the very top, the position of GAD2 is shown in chromosome 2 (red line). The next track down shows annotations giving the context of known gene model for GAD2, and lower we see the reads that aligned to this region of the chromosome. This visualization uses IGV.js which is a complex offering significant functionality; these advanced features can be accessed using the gears to the right of the tracks.